Importance of metabolic coupling for the dynamics of gene expression following a diauxic shift in Escherichia coli

Valentina Baldazzi 1 Delphine Ropers 2 Johannes Geiselmann 2, 3, 4 Daniel Kahn 5 Hidde de Jong 2
2 IBIS - Modeling, simulation, measurement, and control of bacterial regulatory networks
LAPM - Laboratoire Adaptation et pathogénie des micro-organismes [Grenoble], Inria Grenoble - Rhône-Alpes, Institut Jean Roget
4 BAMBOO - An algorithmic view on genomes, cells, and environments
Inria Grenoble - Rhône-Alpes, LBBE - Laboratoire de Biométrie et Biologie Evolutive - UMR 5558
Abstract : Gene regulatory networks consist of direct interactions, but also include indirect interactions mediated by metabolism. We investigate to which extent these indirect interactions arising from metabolic coupling influence the dynamics of the system. To this end, we build a qualitative model of the gene regulatory network controlling carbon assimilation in Escherichia coli, and use this model to study the changes in gene expression following a diauxic shift from glucose to acetate. In particular, we compare the relative variation in the steady-state concentrations of enzymes and transcription regulators during growth on glucose and acetate, as well as the dynamic response of gene expression to the exhaustion of glucose and the subsequent assimilation of acetate. We find significant differences between the dynamics of the system in the absence and presence of metabolic coupling. This shows that interactions arising from metabolic coupling cannot be ignored when studying the dynamics of gene regulatory networks.
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Journal articles
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https://hal.inria.fr/hal-00762570
Contributor : Hidde de Jong <>
Submitted on : Friday, December 7, 2012 - 1:39:17 PM
Last modification on : Wednesday, November 20, 2019 - 2:34:48 AM

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Valentina Baldazzi, Delphine Ropers, Johannes Geiselmann, Daniel Kahn, Hidde de Jong. Importance of metabolic coupling for the dynamics of gene expression following a diauxic shift in Escherichia coli. Journal of Theoretical Biology, Elsevier, 2012, 295, pp.100-115. ⟨10.1016/j.jtbi.2011.11.010⟩. ⟨hal-00762570⟩

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